LAMMPS (13 Oct 2016)
# sample LAMMPS input script for thermal conductivity of liquid LJ
# use fix heat to add/subtract energy from 2 regions

# settings

variable	x equal 10
variable	y equal 10
variable	z equal 20

variable	rho equal 0.6
variable        t equal 1.35
variable	rc equal 2.5

#variable	rho equal 0.85
#variable        t equal 0.7
#variable	rc equal 3.0

# setup problem

units		lj
atom_style	atomic

lattice		fcc ${rho}
lattice		fcc 0.6
Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
region		box block 0 $x 0 $y 0 $z
region		box block 0 10 0 $y 0 $z
region		box block 0 10 0 10 0 $z
region		box block 0 10 0 10 0 20
create_box	1 box
Created orthogonal box = (0 0 0) to (18.8207 18.8207 37.6414)
  2 by 1 by 4 MPI processor grid
create_atoms	1 box
Created 8000 atoms
mass		1 1.0

velocity	all create $t 87287
velocity	all create 1.35 87287

pair_style	lj/cut ${rc}
pair_style	lj/cut 2.5
pair_coeff	1 1 1.0 1.0

neighbor	0.3 bin
neigh_modify	delay 0 every 1

# heat layers

region          hot block INF INF INF INF 0 1
region          cold block  INF INF INF INF 10 11
compute         Thot all temp/region hot
compute         Tcold all temp/region cold

# 1st equilibration run

fix             1 all nvt temp $t $t 0.5
fix             1 all nvt temp 1.35 $t 0.5
fix             1 all nvt temp 1.35 1.35 0.5
thermo	        100
run             1000
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4 -> bins = 14 14 27
Memory usage per processor = 2.55761 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0         1.35   -4.1241917            0   -2.0994448   -3.1961612 
     100    1.1819832   -3.7640881            0    -1.991335   0.53985757 
     200    1.2578365   -3.7395333            0   -1.8530144   0.69591862 
     300    1.3282971   -3.7215427            0   -1.7293461   0.79036065 
     400    1.3714367   -3.7043826            0   -1.6474847   0.85873226 
     500    1.3590952   -3.6707735            0   -1.6323855   0.99602024 
     600    1.3575117   -3.7118244            0   -1.6758114   0.81454305 
     700    1.3284444   -3.7075488            0   -1.7151313   0.81136596 
     800    1.3419995   -3.7155648            0   -1.7028172   0.82925676 
     900    1.3562214   -3.6965609            0   -1.6624831   0.88908117 
    1000    1.3732017   -3.7100044            0   -1.6504594   0.83982701 
Loop time of 0.872163 on 8 procs for 1000 steps with 8000 atoms

Performance: 495320.223 tau/day, 1146.575 timesteps/s
99.5% CPU use with 8 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.48598    | 0.49768    | 0.50892    |   1.1 | 57.06
Neigh   | 0.22855    | 0.23236    | 0.23463    |   0.5 | 26.64
Comm    | 0.082584   | 0.093727   | 0.10748    |   2.9 | 10.75
Output  | 0.0002718  | 0.00028038 | 0.00031757 |   0.1 |  0.03
Modify  | 0.028934   | 0.031425   | 0.03322    |   0.8 |  3.60
Other   |            | 0.01668    |            |       |  1.91

Nlocal:    1000 ave 1020 max 982 min
Histogram: 1 0 2 1 0 1 1 1 0 1
Nghost:    2299.5 ave 2331 max 2268 min
Histogram: 1 1 1 1 0 0 0 3 0 1
Neighs:    27122 ave 28382 max 26337 min
Histogram: 2 0 2 1 1 0 0 1 0 1

Total # of neighbors = 216976
Ave neighs/atom = 27.122
Neighbor list builds = 162
Dangerous builds = 0

velocity	all scale $t
velocity	all scale 1.35

unfix		1

# 2nd equilibration run

fix		1 all nve
fix             hot all heat 1 100.0 region hot
fix             cold all heat 1 -100.0 region cold

thermo_style    custom step temp c_Thot c_Tcold
thermo	        1000
run             10000
Memory usage per processor = 2.55761 Mbytes
Step Temp c_Thot c_Tcold 
    1000         1.35     1.431295    1.2955644 
    2000    1.3518468    1.5562602     1.154905 
    3000    1.3477229    1.5890075    1.2395414 
    4000    1.3487175    1.5491615    1.2019696 
    5000    1.3594394    1.5780597    1.1824492 
    6000    1.3583923     1.541735    1.1675586 
    7000    1.3700321    1.6735877    1.1279114 
    8000    1.3631993    1.6367675    1.0697225 
    9000    1.3739201    1.6846211    1.1138829 
   10000    1.3751455    1.8039471    1.1500399 
   11000    1.3716416     1.833336    1.1267278 
Loop time of 10.3395 on 8 procs for 10000 steps with 8000 atoms

Performance: 417815.278 tau/day, 967.165 timesteps/s
99.5% CPU use with 8 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 4.2189     | 4.9657     | 5.6225     |  25.3 | 48.03
Neigh   | 2.1359     | 2.4223     | 2.6741     |  14.8 | 23.43
Comm    | 0.83801    | 1.6773     | 2.6984     |  57.1 | 16.22
Output  | 0.00042701 | 0.00046191 | 0.00052905 |   0.1 |  0.00
Modify  | 1.0143     | 1.0895     | 1.1846     |   5.7 | 10.54
Other   |            | 0.1844     |            |       |  1.78

Nlocal:    1000 ave 1131 max 878 min
Histogram: 3 1 0 0 0 0 0 1 1 2
Nghost:    2312.88 ave 2525 max 2114 min
Histogram: 2 2 0 0 0 0 0 1 1 2
Neighs:    27457 ave 33797 max 21031 min
Histogram: 3 1 0 0 0 0 0 0 1 3

Total # of neighbors = 219656
Ave neighs/atom = 27.457
Neighbor list builds = 1691
Dangerous builds = 0

# thermal conductivity calculation

compute		ke all ke/atom
variable	temp atom c_ke/1.5

compute         layers all chunk/atom bin/1d z lower 0.05 units reduced
fix		2 all ave/chunk 10 100 1000 layers v_temp file profile.heat

variable        tdiff equal f_2[11][3]-f_2[1][3]
fix             ave all ave/time 1 1 1000 v_tdiff ave running start 13000
thermo_style    custom step temp c_Thot c_Tcold v_tdiff f_ave

run             20000
Memory usage per processor = 2.8078 Mbytes
Step Temp c_Thot c_Tcold v_tdiff f_ave 
   11000    1.3716416     1.833336    1.1267278            0            0 
   12000    1.3703433    1.7829467    1.1194444  -0.66044316            0 
   13000    1.3686734    1.8334366    1.1193477  -0.71431978  -0.71431978 
   14000    1.3856987    1.8048077    1.1052708  -0.73112558  -0.72272268 
   15000    1.3820117    1.7460559     1.110725  -0.72927647  -0.72490728 
   16000    1.3911309     1.923603    1.1161499  -0.77407515  -0.73719925 
   17000    1.3841301    1.7276486    1.0283807  -0.77278638  -0.74431667 
   18000    1.3888918    1.7944951    1.0532944  -0.75665895  -0.74637372 
   19000    1.3876032     1.838174     1.059715  -0.71342263  -0.74166642 
   20000    1.3724644    1.8297128    1.1439176  -0.77352223   -0.7456484 
   21000    1.3798921    1.7968403    1.0288381  -0.70077132  -0.74066206 
   22000    1.3763952    1.8202225    1.0658157  -0.75629111  -0.74222496 
   23000    1.3911378    1.8691478     1.018589  -0.76094865  -0.74392711 
   24000    1.3867754    1.7826523      1.09347  -0.80367344  -0.74890597 
   25000     1.385877    1.9029313    1.0815131  -0.73559505  -0.74788206 
   26000    1.3791773    1.8904022    1.0151678   -0.7729123  -0.74966993 
   27000    1.3800063     1.729283     1.127594  -0.71473941  -0.74734123 
   28000    1.3757197    1.7823772     1.084523  -0.73849831  -0.74678855 
   29000    1.3777555    1.8287284    1.0715132  -0.70375514  -0.74425717 
   30000    1.3821118    1.7382856    1.1078333  -0.79892499  -0.74729427 
   31000    1.3870476    1.8410063    1.1235958  -0.76218423  -0.74807795 
Loop time of 22.4057 on 8 procs for 20000 steps with 8000 atoms

Performance: 385616.132 tau/day, 892.630 timesteps/s
99.3% CPU use with 8 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 7.6116     | 10.003     | 12.262     |  64.3 | 44.65
Neigh   | 4.038      | 4.9528     | 5.8822     |  37.6 | 22.10
Comm    | 1.6649     | 4.7143     | 7.6339     | 124.9 | 21.04
Output  | 0.00098443 | 0.0017504  | 0.0018921  |   0.7 |  0.01
Modify  | 2.1819     | 2.3289     | 2.6598     |  12.6 | 10.39
Other   |            | 0.4047     |            |       |  1.81

Nlocal:    1000 ave 1134 max 850 min
Histogram: 2 1 0 1 0 0 0 1 0 3
Nghost:    2307.75 ave 2561 max 2083 min
Histogram: 4 0 0 0 0 0 0 0 2 2
Neighs:    27561.1 ave 34071 max 19891 min
Histogram: 2 1 1 0 0 0 0 0 1 3

Total # of neighbors = 220489
Ave neighs/atom = 27.5611
Neighbor list builds = 3442
Dangerous builds = 0
Total wall time: 0:00:33
